# HG changeset patch
# User lecorguille
# Date 1554824199 14400
# Node ID 636e36a64d31b66c7635f7228bd5868abe1ba35c
# Parent  b6a8143c397c526eb0817705ed60fe5f44773bcc
planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546

diff -r b6a8143c397c -r 636e36a64d31 README.rst
--- a/README.rst	Fri Feb 01 11:29:35 2019 -0500
+++ b/README.rst	Tue Apr 09 11:36:39 2019 -0400
@@ -2,9 +2,10 @@
 Changelog/News
 --------------
 
-**Version 2.2.5 - 01/02/2019**
+**Version 2.2.5 - 09/04/2019**
 
 - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
 
 **Version 2.2.4 - 09/10/2018**
 
diff -r b6a8143c397c -r 636e36a64d31 abims_CAMERA_annotateDiffreport.xml
--- a/abims_CAMERA_annotateDiffreport.xml	Fri Feb 01 11:29:35 2019 -0500
+++ b/abims_CAMERA_annotateDiffreport.xml	Tue Apr 09 11:36:39 2019 -0400
@@ -200,15 +200,15 @@
         </data>
         <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
             <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" visible="true" />
+            <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
         </collection>
 
-        <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport.pdf" from_work_dir="tabular.zip">
+        <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.pdf" from_work_dir="tabular.zip">
             <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
         </data>
         <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
             <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" visible="true" />
+            <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" />
         </collection>
     </outputs>
 
@@ -442,9 +442,12 @@
 Changelog/News
 --------------
 
-**Version 2.2.5 - 01/02/2019**
+.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
+
+**Version 2.2.5 - 09/04/2019**
 
 - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
 
 **Version 2.2.4 - 09/10/2018**
 
diff -r b6a8143c397c -r 636e36a64d31 lib.r
--- a/lib.r	Fri Feb 01 11:29:35 2019 -0500
+++ b/lib.r	Tue Apr 09 11:36:39 2019 -0400
@@ -36,13 +36,13 @@
 #@author G. Le Corguille
 #The function create a zip archive from the different png generated by diffreport
 diffreport_png2zip <- function() {
-    zip("eic.zip",dir(pattern="_eic"))
-    zip("box.zip",dir(pattern="_box"))
+    zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip"))
+    zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip"))
 }
 
 #The function create a zip archive from the different tabular generated by diffreport
 diffreport_tabular2zip <- function() {
-    zip("tabular.zip",dir(pattern="tabular/*"))
+    zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip"))
 }
 
 #@author G. Le Corguille
@@ -152,7 +152,7 @@
                         diffrep=diffrep[order(diffrep$pvalue), ]
                     }
 
-                    dir.create("tabular")
+                    dir.create("tabular", showWarnings = FALSE)
                     write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
 
                     if (listArguments[["eicmax"]] != 0) {
diff -r b6a8143c397c -r 636e36a64d31 macros.xml
--- a/macros.xml	Fri Feb 01 11:29:35 2019 -0500
+++ b/macros.xml	Tue Apr 09 11:36:39 2019 -0400
@@ -2,12 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.4_2">r-snow</requirement>
-            <requirement type="package" version="3.0.0">bioconductor-xcms</requirement>
-            <requirement type="package" version="1.34.0">bioconductor-camera</requirement>
-            <requirement type="package" version="2.28.0">bioconductor-multtest</requirement>
+            <requirement type="package" version="0.4_3">r-snow</requirement>
+            <requirement type="package" version="1.38.1">bioconductor-camera</requirement>
+            <requirement type="package" version="2.38.0">bioconductor-multtest</requirement>
             <requirement type="package" version="1.1_4">r-batch</requirement>
-            <requirement type="package" version="1.3.23">graphicsmagick</requirement>
+            <requirement type="package" version="1.3.26">graphicsmagick</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
diff -r b6a8143c397c -r 636e36a64d31 planemo_test.sh
--- a/planemo_test.sh	Fri Feb 01 11:29:35 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-# Example of planemo command to launch test
-
-# Note: --galaxy_branch "dev" is set to deal with zip file
-
-
-# -- Use of installed package environments
-# after having installing package on a local galaxy instance
-source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh
-source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh
-planemo test --install_galaxy
-
-#All 1 test(s) executed passed.
-#abims_CAMERA_annotateDiffreport[0]: passed
-
-
-# -- Use of conda dependencies
-planemo conda_init --conda_prefix /tmp/mc
-planemo conda_install --conda_prefix /tmp/mc . 
-planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
-
-#All 1 test(s) executed passed.
-#abims_CAMERA_annotateDiffreport[0]: passed
-
-
-# -- Use of shed_test
-planemo shed_test --install_galaxy -t testtoolshed 
-
-#All 1 test(s) executed passed.
-#testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: passed